Ion beam bombardment induced self-assembly represents a new promising nanofabrication technology due to its advantages of fabricating ordered arrays of uniform nanodots over large area in a rapid process and at low cost. In this thesis, systematic studies have been carried out to investigate the effects of important ion beam parameters on the formation of regular arrays of uniform-sized nanodots. We experimentally demonstrated self-ordered nanodots of uniform size over large area at wafer level. This self-assembly technology also offers potential application for low cost fabrication of magnetic patterned media, which has long been considered as one of the most promising technologies to ultrahigh magnetic data storage density of beyond Tera-bits per square inch. Nanopatterned magnetic films of [Co/Pd]n multilayer and FePt alloy have been achieved on self-assembled substrates. Magnetic and structural properties have been studied.